Genomics approaches aim to identify all functional elements in the human genome and to understand their functions. Such large-scale approaches are thought to greatly increase insights in human biology and disease. Here it is proposed to further develop and validate a new and unique methodology to identify functional elements in the human genome. The approach is based on the hypothesis that direct physical interactions between sequence elements will point to functional relationships between them. For example, regulatory elements have been shown to physically interact with their target genes to control transcription. Similar long-range interactions between genomic elements are thought to be involved in other genomic processes such as DNA replication, repair, meiotic recombination and chromosome condensation. Therefore, identification of chromosomal interactions, and chromosome structural features in general may result in finding functional elements. This proposal entails the further development and validation of an approach that relies on determination and computational analysis of chromosomal interactions as a means to identify functional elements. Chromosomal interactions will be measured using a molecular methodology, "Chromosome Conformation Capture" or "3C" that we have developed. The main goal of this proposal is to assess the use of this structural approach to find functional elements. Specific Aim 1: Development of robust 3C-based strategies to identify functional elements in the human genome. Specific Aim 2: To generate two focused interaction frequency datasets for regions selected by the ENCODE project. Specific Aim 3: To interpret 3C interaction frequency datasets by building structural models. Analysis of the data obtained and integration of these data with results derived from other ENCODE projects is expected to provide information regarding the suitability of this chromosome structural approach to find functional elements.